DreINT0049571 @ danRer10
Intron Retention
Gene
ENSDARG00000069093 | col2a1a
Description
collagen, type II, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-980526-192]
Coordinates
chr8:21177884-21178158:+
Coord C1 exon
chr8:21177884-21177937
Coord A exon
chr8:21177938-21178104
Coord C2 exon
chr8:21178105-21178158
Length
167 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGC
5' ss Score
3.69
3' ss Seq
TCTTTTCATCATCCTACTAGGGT
3' ss Score
7.56
Exon sequences
Seq C1 exon
GGTGAAACTGGTCCTATTGGTTCAATTGGTGCTCCTGGTGCTCGTGGTGCCCCT
Seq A exon
GTAAGCAAACACTTGATTGTCTTTTGTTCAGCGTAAACGGGAATCGTTAGTGCAATGTATTAACCTTGCAGCTAGACAGCTAAAAGATGTACAAAAGGATGTTTGTGGTTTTGTGAAGTGTAAAATTAGTTTTGGTGTTAATCAATATCTTTTCATCATCCTACTAG
Seq C2 exon
GGTGATCGTGGTGAGATTGGTGCACCTGGACCTGCTGGCTTTGCTGGACCCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069093:ENSDART00000100234:37
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(5.6=22.2),PF0139113=Collagen=FE(22.4=100)
A:
NA
C2:
PF0139113=Collagen=FE(22.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGAAACTGGTCCTATTGGTTCA
R:
GGGGTCCAGCAAAGCCAG
Band lengths:
106-273
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]